Fortuna, for whatever reason, thought that ships slow down after their engines are turned off. I was fairly certain this is incorrect but I wanted to make sure:
and sure enough the ship keeps exactly the velocity you had while being powered off. You can even orbit planets thanks to this. Keep in mind turning the throttle to zero is NOT the same as turning the engines off. If IFCS is still on, it will slow your ship to a stop with the throttle at zero, which is what I think Fortuna was actually doing and then complaining about the "unrealistic" flight model.